Proper regulation of RNA Polymerase II (RNAPII) transcription is required for proper gene expression levels and the maintenance of overall genome stability. The regulation of RNAPII is altered in the pathogenesis of many human diseases including cancer, neurological disorders, and viral infection. In order to combat changes in RNAPII transcription during the course of disease progression, the basic mechanisms that underlie the regulation of RNAPII must be understood. We have identified a novel regulator of RNAPII, an atypical protein phosphatase known as Rtr1 that is conserved from yeast to humans. We have shown that Rtr1 is required for dephosphorylation of a specific serine in a conserved domain in RNAPII known as the CTD. However, the mechanisms that require CTD dephosphorylation during transcription are not understood. In order to determine the precise role of Rtr1 during RNAPII transcription, we will focus on three specific questions: (1) Is Rtr1-dependent CTD dephosphorylation required for recruitment of the mRNA 3' end processing machinery? (2) Does Rtr1-dependent dephosphorylation stimulate the release of phospho-CTD binding proteins? and (3) Does Rtr1 regulate the phosphorylation status of other protein complexes involved in the regulation of RNAPII transcription elongation and termination? By addressing these key questions, we will increase our understanding of the fundamental process of RNAPII transcription which will allow us to define how defects in this process cause human disease.